Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	5,122,692	A→C	29.2%	L80R (CTG→CGG)	slyA_2 ←	Transcriptional regulator SlyA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	5,122,692	0	A	C	29.2%	61.8 / 2.8	49	L80R (CTG→CGG)	slyA_2	Transcriptional regulator SlyA
Reads supporting (aligned to +/- strand):  ref base A (16/15);  new base C (7/9);  total (23/26)
Fisher's exact test for biased strand distribution p-value = 7.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACGCCGGTAAACAGCTCTACCCGCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCGAAGCGGGCCAGGTGCAGCAACACCAGCCAGCGCG  >  KT2440/5122562‑5122821                                                                                                                                   |                                                                                                                                  cACGCCGGTAAACAGCTCTACCCGCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGccc                                                                                                                               <  6:235632/135‑1 (MQ=255) cACGCCGGTAAACAGCTCTACCCGCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTCCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGccc                                                                                                                               <  7:40954/135‑1 (MQ=255)     ccGGTAAAAAGCTCTACCCGCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTgc                                                                                                                           >  5:353759/1‑135 (MQ=255)           aaCAGCTCTACCCGCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCCGCCCCGCCTGCCGGCGCACCCGCCCTTGCGCtt                                                                                                                       >  7:76039/1‑133 (MQ=255)                   tACCCGCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGCTCCTCCCGCCCCGCCCGCCGGCGCCCCCGCCCGTGCGCTTCCCGGCTGTc                                                                                                             >  2:152987/1‑135 (MQ=255)                   tACCCGCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTc                                                                                                             >  7:288049/1‑135 (MQ=255)                   tACCCGCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCg                                                                                                            >  3:79485/1‑136 (MQ=255)                      ccgccgGTGGTTGGCGATGGTCTCGATCTGAGCGATCACCGGCTTGGCCGGCGGCCACAGTCAAATCTGCTTCGCCCGCCGAACCTCCCGCACGGCCTGCCGGCGCACCAGCCCTTGCGCTGCCAGGCTGTCGTGc                                                                                                         <  4:79392/136‑1 (MQ=255)                       cGCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGc                                                                                                         <  6:353759/135‑1 (MQ=255)                        gCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCCGCCCTTGCGCTTCCAGGCTGTCGAGCa                                                                                                        >  6:133502/1‑135 (MQ=255)                           gCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGAcg                                                                                                    >  3:117420/1‑136 (MQ=255)                             tGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGCTCCTCCAGCCCCGCCTGCCGGCGCACCCGCCCTTGCGCTTCCAGGCTGTCGAGCAGAcgc                                                                                                   >  2:340233/1‑135 (MQ=255)                             tGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCCGccc                                                                                                                               >  8:279794/1‑107 (MQ=255)                             tGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGccc                                                                                                                               <  7:279794/107‑1 (MQ=255)                             tGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCGTCCAGGCTGTCGCGCAGAcgc                                                                                                   >  8:76628/1‑135 (MQ=255)                                      aTGGTCTCGATCTGATCGATCACCGGGTGGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGACCCTCCACCACCGCCTGCCGGCGCACCCGCCCTTGCGCTTCCAGGCTGGCGCGCAGACGCGCCAGGGTc                                                                                          <  8:145972/135‑1 (MQ=255)                                      aTGGTCTCGATCTGATCGATCAACGGCTGGGCCGGCGGGAACAGTACAATCTTCTTCGCCCGCCGATCCGCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTc                                                                                          <  7:129599/135‑1 (MQ=255)                                           ctcGAGCTGATCGATCACCGGCTGGGCGGGCGGGCACAGTACAATCTGCTTCGCCCGCCGATCCTCCAGCCCCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGcc                                                                                     <  6:82677/135‑1 (MQ=255)                                             cGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCtt                                                                                   >  6:156136/1‑135 (MQ=255)                                               aTCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCtt                                                                                   <  2:106338/133‑1 (MQ=255)                                                       gatcAACGGCTTGGCCCGCGGGCACAGTACAATAGTCTTCGCCCGCCCATCCTCCAGCCCCGCCTGCCGGCGCCCCCCCCCTGGCGCTTCCAGGCTGTCGCGCCGACGCGCCAGGGTCGGGCCTTCGCCGCCTAcc                                                                        >  4:7018/1‑135 (MQ=255)                                                          caccGGCTGGGCCGGCGGGCACATTACAATCTGCTTCGCCCGCGGAGCCTCCCGCACCGCCTCCCGGCGCACCCGCCCTTGCGCTTCCCGGCTGGCGCGCACCCGCGCCAGGGTCGGGCCTTCGACGCCTACg                                                                        <  1:14647/130‑1 (MQ=255)                                                           accGGCTTGGCCGGCGGGCACAGTAAAATCTTCTTCGCCCGCGGATCCCCCACCCCCGCCTGCCGGCGCACCCCCCCTGGCGCGTCCAGGGTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGctct                                                                    <  3:133074/134‑1 (MQ=255)                                                           aaCGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCCGCCCTTGCGCTTCCCGGCTGTCGACCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGctct                                                                    <  4:176310/136‑1 (MQ=255)                                                            gcGGCTTGGCCGGCGGCCACAGTACAATCTTCTTCGCCCGCCGATCCTCGACCACCGCCTGCCGGGGCACCTGGCATTGCGGTGCCCGGCTGGCCCGCAGACGCGCCAGGGGCGGGCCTTCGACGCCTACGctct                                                                    <  8:183862/134‑1 (MQ=255)                                                            aCGGCTTGGCGGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGctct                                                                    <  8:83499/135‑1 (MQ=255)                                                            aCGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACg                                                                              >  1:45877/1‑125 (MQ=255)                                                            aCGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACg                                                                              <  2:45877/125‑1 (MQ=255)                                                            aCGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCACCACCGCCGGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGctct                                                                    <  7:271336/135‑1 (MQ=255)                                                                 ttGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCCGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGcc                                                               >  6:369414/1‑135 (MQ=255)                                                                      gggggggCACATTACAATCTTCTGCGCCCGCCGAGCCCCCCCCCCCGCCTGCGGGCGCACCCGCCGTTGGGCTTCCCGGGTGTCGCGCCGACGCGCCAGGGGCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTc                                                          <  6:203403/131‑1 (MQ=255)                                                                      gggcggGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCCCCGCCGGCCGGCGCACCCGCCCTTGCGCTGCCAGGCGGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTc                                                          <  1:7249/134‑1 (MQ=255)                                                                      cggcggGCACAGTACAATCTTCTGCGCCCGCCGATCCTCCAGCACCGCCGGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGGCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTc                                                          <  2:104389/135‑1 (MQ=255)                                                                                     aaTCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGTCGCACAAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCGTTGTCGGGGc                                           >  1:22574/1‑135 (MQ=255)                                                                                     aaTCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGc                                           >  8:199282/1‑135 (MQ=255)                                                                                              cgcccgccGAGCCTCCAGCCCCGCCGGCCGGCGCACCTGCCCTTGCGCTTCCAGGCTGTCGCGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCg                                    <  3:145807/133‑1 (MQ=255)                                                                                               gcccgccGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGAcgc                                                                                                   >  7:344276/1‑69 (MQ=255)                                                                                               gcccgccGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGAcgc                                                                                                   <  8:344276/69‑1 (MQ=255)                                                                                               gcccgccGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCGAAg                                 >  1:74003/1‑135 (MQ=255)                                                                                               gcccgccGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCGAAg                                 >  8:162082/1‑135 (MQ=255)                                                                                               gcccgccGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCGAAg                                 >  1:256661/1‑135 (MQ=255)                                                                                               gcccgccGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCGTCTTCGAAg                                 >  1:68951/1‑135 (MQ=255)                                                                                               gccccccGATCCGCCCCCACCGCCGGCGGGCGCACCCGCCGTCGCGCTCCCCGGCTGCCCAGCACACGCGCCAGGGGCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCg                                    <  5:34503/132‑1 (MQ=255)                                                                                                 ccgccgATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCGAAGCg                               >  1:287377/1‑135 (MQ=255)                                                                                                     cgATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGCGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCGAAGCGGGcc                           <  8:288049/135‑1 (MQ=255)                                                                                                     cgACCCTCCCCCACCGCCTGCCGCCGCCCCCGCCCGGCCGCTTCCAGCCTGGGGCGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCGAAGCGGGcc                           <  6:368616/135‑1 (MQ=255)                                                                                                                        gCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCGTCTTCGCAGCGGGCCCGGTGCAGCCACAccag          >  5:361530/1‑133 (MQ=255)                                                                                                                          cGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCGAAGCGGGCCAGGTGCAGCAACAccagcc        <  6:180926/133‑1 (MQ=255)                                                                                                                             cgcACCCGCCCTTGCGCTTCCCGGGTGCCGCCCATCCGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCGAAGCGGGCCAGGTGCAGCAACACCAGCCAgcgcg  <  3:216654/136‑1 (MQ=255)                                                                                                                                   |                                                                                                                                  CACGCCGGTAAACAGCTCTACCCGCAGCTGGTTGGCGATGGTCTCGATCTGATCGATCAACGGCTTGGCCGGCGGGCACAGTACAATCTTCTTCGCCCGCCGATCCTCCAGCACCGCCTGCCGGCGCACCAGCCCTTGCGCTTCCAGGCTGTCGAGCAGACGCGCCAGGGTCGGGCCTTCGACGCCTACGCTCTGGGCCAGCTCACGCTGTGTCGGGGCTTCTTCGAAGCGGGCCAGGTGCAGCAACACCAGCCAGCGCG  >  KT2440/5122562‑5122821

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑